Single nucleotide polymorphisms (SNPs) are useful as biomarkers for predicting disease susceptibility or progression, or as a guide for individualized therapy, including drug therapy.
ACE—
Angiotensin I-converting enzyme (ACE) plays a key role in cardiovascular biology. Its functions include formation of angiotensin II and inactivation of bradykinin, resulting in vasoconstriction and increased blood pressure. ACE inhibitors are recommended as first-line treatment of hypertension and heart failure. Expressed in many tissues, ACE further affects a broad spectrum of physiological processes. As a result, the ACE gene has been implicated in susceptibility to hypertension, myocardial infarction, renal pathophysiology, diabetes, and Alzheimer's disease.
In particular, angiotensin I-converting enzyme (ACE1) is expressed with a wide tissue distribution including plasma, endothelial cells, kidney, heart and lungs. This enzyme hydrolyzes a number of substrates, including conversion of angiotensin I to angiotensin II (as part of the renin-angiotensin system). Angiotensin II (AngII) is a potent vasoconstrictor and pro-hypertrophic factor. Ang II induces production of superoxide free radicals (O2−) that scavenge available nitric oxide and reduce endothelial vasodilatation. ACE1 has even greater affinity for bradykinin, thus hydrolyzing and inactivating a potent vasodilator. Through these pathways, ACE1 exerts potent physiological influence over salt balance, blood volume and blood pressure levels with significant implications for cardiovascular disease in particular.
Targeted reduction of ACE1 via the blockbuster drug class of ACE inhibitors that directly bind the active site of the ACE protein is a first line anti-hypertensive treatment for heart disease. ACE inhibitors decrease the release of aldosterone and retention of salt and water, significantly lowering blood pressure. Drugs in this class have been shown to reduce mortality in many large clinical trials. These drugs are often administered immediately following myocardial infarction. They currently represent a major pharmaceutical class with millions of prescriptions worldwide, with additional indications in hypertension or renal crisis in relation to scleroderma, and prevention of kidney damage in some diabetics. Furthermore, recent literature indicates that ACE1 may play a role in the degradation of Alzheimer's plaques making it a possible disease factor (26,39).
It has been determined that there is variability in patient responses to ACE inhibitor treatment. Family-based studies over the last two decades indicate that ACE1 levels as a quantitative phenotype are strongly influenced by a genetic component that maps to the ACE1 locus; however, well-supported functional variants remain to be identified (40, 1, 11). Nonetheless, this has been considered one of the most compelling examples in human genetics of a single gene contributing to variability in a complex human trait. Intolerance for ACE inhibitors is as high as 20%, with the most common side effect being a severe cough, especially in Asian patients (41).
Moreover, studies in African-American patients on ACE inhibitors indicated they received less benefit (16) and increased risk of side effects (4-5 fold) (18) and mortality from angioedema (42-45), suggesting a possible pharmacogenetic influence on drug response. An intron 16 ALU insertion-deletion polymorphism of 287 bp has been extensively studied, because it revealed significant associations in a number of studies. However, several research groups have shown that this polymorphism is unlikely to have any direct functional role (5,4) and, instead, is likely in linkage to one or more true, and as yet undetermined, functional variants. Studies employing diverse populations and public data from the HapMap project indicate the ALU polymorphism alone is an inadequate proxy for the genetic diversity at this gene locus. However, there are thousands of studies genotyping solely the ALU polymorphism in a variety of clinical populations. These demonstrate both positive and negative associations, as reflected in metanalyses of this variant (3). Since these previous studies rely on the assumption that the ALU polymorphism is completely or highly linked to true functional variants, they may be missing critical information if this assumption is incorrect or only partially correct. For example, one study of outcomes in 38,000 individuals receiving ACE inhibitor treatment genotyped only the ALU polymorphism and found no significant association (2).
The suggestion of a heritable component to serum ACE activity (1) led to extensive phenotype-genotype studies with ACE-related pathophysiology and response to ACE inhibitors (2). Numerous studies have focused on an insertion/deletion (I/D) polymorphism in intron 15. However, meta-analyses of phenotypic associations largely failed to confirm a role for I/D (3), and in vitro experiments did not reveal any effect on transcription (4) or splicing (5). Therefore, genetic factors contributing to differential ACE expression remain uncertain.
What are lacking are tools for predicting the likelihood that a particular patient will be responsive to a therapeutic ACE, and in particular, identifying agents to which the ACE will be sensitive or resistant. Also lacking are tools for profiling genetic factors influencing sensitivity and resistance of patients to ACE therapeutic agents. Such tools, and the resulting gene expression profiles, would be predictive of treatment response of a patient to a particular drug, and would allow for increased predictability regarding chemosensitivity or chemoresistance of such patients to enable the design of optimal treatment regimens for patients.
SOD2—
Oxidative stress and damage play a role in the pathogenesis of a number of diseases. In particular, mitochondrial-derived oxidants play an important role in the pathogenesis of many human disorders.
SOD2 is an antioxidant, the mitochondrial form of SOD and an important defense against oxidative damage. The SOD2 gene is a member of the iron/manganese superoxide dismutase family. The mitochondrial superoxide dismutase protein (SOD2) serves a critical cellular role in protecting from harmful reactive species by reducing these species to hydrogen peroxide (H2O2) which is then processed to hydroxide (OH) and then water (H2O). This is a normal cellular process that is critical to life and protects the integrity of cellular genomes. Under conditions of stress including disease and environmental conditions (e.g., toxins) reactive species can accumulate to a degree that overwhelms the capacity of endogenous protectors including SOD2. Thus, if common alleles exist that affect SOD2 production these alleles may contribute to many diseases, but may only be important under conditions of accumulated oxidative stress.
What are lacking are tools for predicting the likelihood that a particular patient will be responsive to a therapeutic SOD2 agent, and in particular, identifying agents to which the SOD2 agent will be sensitive or resistant.
Also lacking are tools for profiling genetic factors influencing sensitivity and resistance of patients to SOD2-caused oxidative damage.
SLC6A3—
Dopamine active transporter (SLC6A3, formerly) is a membrane-spanning protein that binds the neurotransmitter dopamine. SLC6A3 provides the primary mechanism through which dopamine is cleared from synapses. SLC6A3 works by transporting dopamine from the synapse into a neuron. SLC6A3 is present in the peri-synaptic area of dopaminergic neurons in areas of the brain where dopamine signaling is common. SLC6A3 terminates the dopamine signal and is implicated in a number of dopamine-related disorders, including alcoholism, attention deficit hyperactivity disorder, bipolar disorder, clinical depression, drug abuse, Parkinson disease, Tourette syndrome and Schizophrenia. Stimulant medications, such as those used to treat ADHD, and drugs of abuse such as amphetamine bind to SLC6A3 and inhibit reuptake of dopamine. Genetic variants of SLC6A3 may influence levels of gene expression and/or ability of drugs to bind to SLC6A3 protein. The gene that encodes the SLC6A3 protein is located on human chromosome 5, consists of 15 coding exons, and is roughly 64 kpb long. It is believed that the associations between SLC6A3 and dopamine related disorders has come from a genetic polymorphism in the SLC6A3 gene, which influences the amount of protein expressed.
What are lacking are tools for predicting the likelihood that a particular patient will be responsive to a therapeutic SLC6A3 agent, and in particular, identifying agents to which the SLC6A3 therapeutic agent will be sensitive or resistant.
CYP2C9—
CYP2C9 (encoding cytochrome P450 2C9) is a liver drug metabolizing enzyme, involved in metabolism of ˜20% of pharmaceuticals. CYP2C9 is a member of the cytochrome P450 mixed-function oxidase system and is involved in the metabolism of xenobiotics in the body. CYP2C9 is involved in the metabolism of several groups of drugs, such as, for example, non-steroidal anti-inflammatory drugs (NSAIDs). Genetic polymorphism exists for CYP2C9 expression and there is a belief that approximately 1-3% of Caucasian populations are poor metabolizers with no CYP2C9 function.
What are lacking are tools for predicting the likelihood that a particular patient will be responsive to a therapeutic CYP2C9 agent, and in particular, identifying agents to which the CYP2C9 agent will be sensitive or resistant.
Such tools would likewise enable the identification of new drugs that modulate expression of genes that affect chemosensitivity, particularly new agents that alter expression of these genes to overcome drug resistance or enhance chemosensitivity.
Additional advantages, objects, and features of the invention will be set forth in part in the description which follows and in part will become apparent to those having ordinary skill in the art upon examination of the following or may be learned from practice of the invention. The objects and advantages of the invention may be realized and attained as particularly pointed out in the appended claims.